Package: RCyjs 2.35.0

Paul Shannon

RCyjs: Display and manipulate graphs in cytoscape.js

Interactive viewing and exploration of graphs, connecting R to Cytoscape.js, using websockets.

Authors:Paul Shannon

RCyjs_2.35.0.tar.gz
RCyjs_2.35.0.zip(r-4.7)RCyjs_2.35.0.zip(r-4.6)RCyjs_2.35.0.zip(r-4.5)
RCyjs_2.35.0.tgz(r-4.6-any)RCyjs_2.35.0.tgz(r-4.5-any)
RCyjs_2.35.0.tar.gz(r-4.7-any)RCyjs_2.35.0.tar.gz(r-4.6-any)
RCyjs_2.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RCyjs/json (API)
NEWS

# Install 'RCyjs' in R:
install.packages('RCyjs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:RCyjs-2.35.0(bioc 3.24)RCyjs-2.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualizationgraphandnetworkthirdpartyclient

4.68 score 48 scripts 388 downloads 88 exports 17 dependencies

Last updated from:0b47368051. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR156
linux-devel-x86_64WARNING190
source / vignettesOK170
linux-release-x86_64WARNING183
macos-release-arm64WARNING90
macos-oldrel-arm64WARNING108
windows-develWARNING93
windows-releaseWARNING95
windows-oldrelWARNING81
wasm-releaseOK104

Exports:addGraphaddGraphFromFileclearSelectioncreateTestGraphdataFramesToJSONdeleteGraphdeleteSelectedNodesedaedaNamesfitfitSelectiongetEdgeCountgetJSONgetLayoutStrategiesgetNodeCountgetNodesgetPositiongetSelectedNodesgetSupportedEdgeDecoratorShapesgetSupportedNodeShapesgetZoomgraphNELtoJSON.stringhAlignhideAllEdgeshideEdgeshideNodeshideSelectedNodesinvertNodeSelectionlayoutlayoutSelectionInGridlayoutSelectionInGridInferAnchorloadStyleFilenoanoaNamesRCyjsreadAndStandardizeJSONNetworkFilereadAndStandardizeJSONStyleFileredrawrestoreLayoutsaveJPGsaveLayoutsavePNGselectFirstNeighborsOfSelectedNodesselectNodessetBackgroundColorsetDefaultEdgeColorsetDefaultEdgeLineColorsetDefaultEdgeLineStylesetDefaultEdgeSourceArrowColorsetDefaultEdgeSourceArrowShapesetDefaultEdgeTargetArrowColorsetDefaultEdgeTargetArrowShapesetDefaultEdgeWidthsetDefaultNodeBorderColorsetDefaultNodeBorderWidthsetDefaultNodeColorsetDefaultNodeFontColorsetDefaultNodeFontSizesetDefaultNodeHeightsetDefaultNodeShapesetDefaultNodeSizesetDefaultNodeWidthsetDefaultStylesetEdgeAttributessetEdgeStylesetGraphsetNodeAttributessetNodeBorderColorsetNodeBorderWidthsetNodeColorsetNodeColorRulesetNodeFontColorsetNodeFontSizesetNodeHeightsetNodeLabelAlignmentsetNodeLabelRulesetNodeShapesetNodeSizesetNodeSizeRulesetNodeWidthsetPositionsetZoomsfnshowAllshowEdgesshowNodessimpleDemoGraphvAlign

Dependencies:base64encBiocGenericsBrowserVizclifastmapgenericsgraphhttpuvjsonlitelaterlifecyclemagrittrotelpromisesR6Rcpprlang

RCyjs: interactive network visualization using cytoscape.js

Paul Shannon

Rendered fromRCyjs.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-04-30
Started: 2018-04-20

Readme and manuals

Help Manual

Help pageTopics
addGraphaddGraph addGraph,RCyjs-method
addGraphFromFileaddGraphFromFile addGraphFromFile,RCyjs-method
clearSelectionclearSelection clearSelection,RCyjs-method
createTestGraphcreateTestGraph
Create a cytoscape.js JSON graph from one or two data.frames.dataFramesToJSON
deleteGraphdeleteGraph deleteGraph,RCyjs-method
deleteSelectedNodesdeleteSelectedNodes deleteSelectedNodes,RCyjs-method
edaeda
edaNamesedaNames
fitfit fit,RCyjs-method
fitSelectionfitSelection fitSelection,RCyjs-method
getEdgeCountgetEdgeCount getEdgeCount,RCyjs-method
getJSONgetJSON getJSON,RCyjs-method
getLayoutStrategiesgetLayoutStrategies getLayoutStrategies,RCyjs-method
getNodeCountgetNodeCount getNodeCount,RCyjs-method
getNodesgetNodes getNodes,RCyjs-method
getPositiongetPosition getPosition,RCyjs-method
getSelectedNodesgetSelectedNodes getSelectedNodes,RCyjs-method
getSupportedEdgeDecoratorShapesgetSupportedEdgeDecoratorShapes getSupportedEdgeDecoratorShapes,RCyjs-method
getSupportedNodeShapesgetSupportedNodeShapes getSupportedNodeShapes,RCyjs-method
getZoomgetZoom getZoom,RCyjs-method
Convert R graphNEL object to cytoscape.js JSON.graphNELtoJSON.string
hAlignhAlign hAlign,RCyjs-method
hideAllEdgeshideAllEdges hideAllEdges,RCyjs-method
hideEdgeshideEdges hideEdges,RCyjs-method
hideNodeshideNodes hideNodes,RCyjs-method
hideSelectedNodeshideSelectedNodes hideSelectedNodes,RCyjs-method
invertNodeSelectioninvertNodeSelection invertNodeSelection,RCyjs-method
layoutlayout layout,RCyjs-method
layoutSelectionInGridlayoutSelectionInGrid layoutSelectionInGrid,RCyjs-method
layoutSelectionInGridInferAnchorlayoutSelectionInGridInferAnchor layoutSelectionInGridInferAnchor,RCyjs-method
loadStyleFileloadStyleFile loadStyleFile,RCyjs-method
noanoa
noaNamesnoaNames
Create an RCyjs object.RCyjs RCyjs RCyjs-class
Read in a JSON network file, identify (or add) elements field return JSONreadAndStandardizeJSONNetworkFile
Read in a JSON file, extract the selector elements, return JSONreadAndStandardizeJSONStyleFile
redrawredraw redraw,RCyjs-method
restoreLayoutrestoreLayout restoreLayout,RCyjs-method
saveJPGsaveJPG saveJPG,RCyjs-method
saveLayoutsaveLayout saveLayout,RCyjs-method
savePNGsavePNG savePNG,RCyjs-method
selectFirstNeighborsOfSelectedNodesselectFirstNeighborsOfSelectedNodes selectFirstNeighborsOfSelectedNodes,RCyjs-method
selectNodesselectNodes selectNodes,RCyjs-method
setBackgroundColorsetBackgroundColor setBackgroundColor,RCyjs-method
setDefaultEdgeColorsetDefaultEdgeColor setDefaultEdgeColor,RCyjs-method
setDefaultEdgeLineColorsetDefaultEdgeLineColor setDefaultEdgeLineColor,RCyjs-method
setDefaultEdgeLineStylesetDefaultEdgeLineStyle setDefaultEdgeLineStyle,RCyjs-method
setDefaultEdgeSourceArrowColorsetDefaultEdgeSourceArrowColor setDefaultEdgeSourceArrowColor,RCyjs-method
setDefaultEdgeSourceArrowShapesetDefaultEdgeSourceArrowShape setDefaultEdgeSourceArrowShape,RCyjs-method
setDefaultEdgeTargetArrowColorsetDefaultEdgeTargetArrowColor setDefaultEdgeTargetArrowColor,RCyjs-method
setDefaultEdgeTargetArrowShapesetDefaultEdgeTargetArrowShape setDefaultEdgeTargetArrowShape,RCyjs-method
setDefaultEdgeWidthsetDefaultEdgeWidth setDefaultEdgeWidth,RCyjs-method
setDefaultNodeBorderColorsetDefaultNodeBorderColor setDefaultNodeBorderColor,RCyjs-method
setDefaultNodeBorderWidthsetDefaultNodeBorderWidth setDefaultNodeBorderWidth,RCyjs-method
setDefaultNodeColorsetDefaultNodeColor setDefaultNodeColor,RCyjs-method
setDefaultNodeFontColorsetDefaultNodeFontColor setDefaultNodeFontColor,RCyjs-method
setDefaultNodeFontSizesetDefaultNodeFontSize setDefaultNodeFontSize,RCyjs-method
setDefaultNodeHeightsetDefaultNodeHeight setDefaultNodeHeight,RCyjs-method
setDefaultNodeShapesetDefaultNodeShape setDefaultNodeShape,RCyjs-method
setDefaultNodeSizesetDefaultNodeSize setDefaultNodeSize,RCyjs-method
setDefaultNodeWidthsetDefaultNodeWidth setDefaultNodeWidth,RCyjs-method
setDefaultStylesetDefaultStyle setDefaultStyle,RCyjs-method
setEdgeAttributessetEdgeAttributes setEdgeAttributes,RCyjs-method
setEdgeStylesetEdgeStyle setEdgeStyle,RCyjs-method
setGraphsetGraph setGraph,RCyjs-method
setNodeAttributessetNodeAttributes setNodeAttributes,RCyjs-method
setNodeBorderColorsetNodeBorderColor setNodeBorderColor,RCyjs-method
setNodeBorderWidthsetNodeBorderWidth setNodeBorderWidth,RCyjs-method
setNodeColorsetNodeColor setNodeColor,RCyjs-method
setNodeColorRulesetNodeColorRule setNodeColorRule,RCyjs-method
setNodeFontColorsetNodeFontColor setNodeFontColor,RCyjs-method
setNodeFontSizesetNodeFontSize setNodeFontSize,RCyjs-method
setNodeHeightsetNodeHeight setNodeHeight,RCyjs-method
setNodelLabelAlignmentsetNodeLabelAlignment setNodeLabelAlignment,RCyjs-method
setNodeLabelRulesetNodeLabelRule setNodeLabelRule,RCyjs-method
setNodeShapesetNodeShape setNodeShape,RCyjs-method
setNodeSizesetNodeSize setNodeSize,RCyjs-method
setNodeSizeRulesetNodeSizeRule setNodeSizeRule,RCyjs-method
setNodeWidthsetNodeWidth setNodeWidth,RCyjs-method
setPositionsetPosition setPosition,RCyjs-method
setZoomsetZoom setZoom,RCyjs-method
sfnsfn sfn,RCyjs-method
showAllshowAll showAll,RCyjs-method
showEdgesshowEdges showEdges,RCyjs-method
showNodesshowNodes showNodes,RCyjs-method
simpleDemoGraphsimpleDemoGraph
vAlignvAlign vAlign,RCyjs-method